SmashCommunity 1.6p2 – Metagenomic Analysis and Annotation Tool

SmashCommunity 1.6p2

:: DESCRIPTION

 SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It comes with built-in support for state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction, and can be easily extended to support additional software. SmashCommunity provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, compare compositions of multiple metagenomes and produce intuitive visual representations of such analyses.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SmashCommunity

:: MORE INFORMATION

Citation

Arumugam, M., Harrington, E. D., Foerstner, K. U., Raes, J. and P. Bork. (2010)
SmashCommunity: A metagenomic annotation and analysis tool,
Bioinformatics, 26, 2977-8.

 

trimAl 1.4 – Tool for Automated Alignment Trimming

trimAl 1.4

:: DESCRIPTION

trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment

::DEVELOPER

Gabaldón’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX / Linux / Windows

:: DOWNLOAD

 trimAl

:: MORE INFORMATION

Citation:

Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon.
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Bioinformatics 2009 25: 1972-1973.

AbundanceBin 1.0.1 – Abundance-based tool for Binning Metagenomic Sequences

AbundanceBin 1.0.1

:: DESCRIPTION

AbundanceBin is an abundance-based tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes—-two important characteristic parameters for a microbial community.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AbundanceBin

:: MORE INFORMATION

Citation:

Yu-Wei Wu and Yuzhen Ye.
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.
Lecture Notes in Computer Science2010, Volume 6044/2010, 535-549 (RECOMB 2010)

STRIKE 1.2 – Sequence Alignment Scoring Tool

STRIKE 1.2

:: DESCRIPTION

STRIKE (Single sTRucture Induced Evaluation) is a program to evaluate protein multiple sequence alignments using a single protein structure.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  STRIKE

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Dec 15;27(24):3385-91. doi: 10.1093/bioinformatics/btr587. Epub 2011 Oct 28.
STRIKE: evaluation of protein MSAs using a single 3D structure.
Kemena C, Taly JF, Kleinjung J, Notredame C.

OptiMAS 1.5 – Decision Support tool to conduct Marker-Assisted Selection programs

OptiMAS 1.5

:: DESCRIPTION

OptiMAS has been developed with the possibility to consider a multi-allelic context,which opens new prospects to further accelerate genetic gain by assembling favorable alleles issued from diverse parents.

:: DEVELOPER

ABI Bioinformatic and Informatic Team 

:: SCREENSHOTS

OptiMAS

:: REQUIREMENTS

  •  Windows / Linux / MacOsX

:: DOWNLOAD

 OptiMAS

:: MORE INFORMATION

Citation:

Valente, F., Gauthier, F., Bardol, N., Blanc, G., Joets, J., Charcosset, A. & Moreau, L. (in prep)
OptiMAS: decision support for marker-assisted selection.

Trebol 20111212 – Interactive Comparative Genomics Tool

Trebol 20111212

:: DESCRIPTION

Trebol is a multi-platform software for comparative genome analyses with functionalities such as sequence retrieving, generation of sequence comparisons, visualization, edition and rendering of high quality images for scientific publications.

::DEVELOPER

Millenium Institute of Oceanography

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

Trebol

:: MORE INFORMATION

eRNA 1.01 – RNA Data Analysis Tool

eRNA 1.01

:: DESCRIPTION

eRNA is an RNA data analysis tool for high-throughput RNA sequencing experiments

::DEVELOPER

eRNA team

:: SCREENSHOTS

eRNA

:: REQUIREMENTS

  • Linux
  • Perl
  • R

:: DOWNLOAD

 eRNA 

:: MORE INFORMATION

Citation:

BMC Genomics. 2014 Mar 5;15:176. doi: 10.1186/1471-2164-15-176.
eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.
Yuan T, Huang X, Dittmar RL, Du M, Kohli M, Boardman L, Thibodeau SN, Wang L

SHOT 2.0 – Shared Ortholog and Gene Order Tree Reconstruction Tool

SHOT 2.0

:: DESCRIPTION

SHOT is a web server for the classification of genomes on the basis of shared gene content or the conservation of gene order that reflects the dominant, phylogenetic signal in these genomic properties. In general, the genome trees are consistent with classical gene-based phylogenies, although some interesting exceptions indicate massive horizontal gene transfer. SHOT is a useful tool for analysing the tree of life from a genomic point of view

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

SHOT: a web server for the construction of genome phylogenies.
Korbel JO, Snel B, Huynen MA, Bork P
Trends Genet. 2002 Mar; 18(3): 158-62. PubMed: 11858840.

KEX 1.21 – A simple Knowledge EXtraction tool

KEX 1.21

:: DESCRIPTION

KEX is a protein name annotation tool based on PROPER (PROtien Proper-noun Extraction Rules)

::DEVELOPER

Ken Ichiro Fukuda (fukuda@cbrc.jp)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • GCC

:: DOWNLOAD

  KEX

:: MORE INFORMATION